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2021-10-28Remove all elasticsearch references in gn2BonfaceKilz
2021-10-28Remove the use of '@deprecated'BonfaceKilz
This causes noisy logging.
2021-10-25utility: redis_tools: Remove dead functionsBonfaceKilz
2021-10-25authentication_tools: Mark `check_owner_or_admin` as deprecatedBonfaceKilz
Use the new auth proxy tools instead.
2021-10-25utility.hmac: Label "hmac_creation" as deprecatedBonfaceKilz
This function is coupled to "wqflask.app", therefore requiring it's import at the module level. This may lead circular importation issues when working with blueprints.
2021-10-25Mark `get_resource_info` as deprecatedBonfaceKilz
2021-10-22Fix line pulling GN3_LOCAL_URL from settingszsloan
2021-10-22Replace hardcoded GN proxy URLs with one pulled from settingszsloan
2021-10-22Added proxy and local GN3 URLs in tools.py (which should be set in the ↵zsloan
settings file)
2021-10-04Changed get_user_groups to pull both the ID and details in the for loop from ↵zsloan
group_list by using group_list.items()
2021-09-10Removed encoding, since it's apparently not needed since the Python 3 ↵zsloan
switchover (and was causing there to be no matches between user IDs and groups)
2021-08-23Account for situations where the minimum permutation value is also above ↵zsloan
webqtlConfig.MAXLRS; previously threw an error
2021-08-20startup_config.py: Add DebugToobarExtension for wsgi DEBUG modeBonfaceKilz
* wqflask/utility/startup_config.py (app_config): Add DebugToolbarExtension
2021-07-12Encode user_id as bytestring if not already bytestring to account for some ↵zsloan
user_ids being stored as different encoding
2021-06-17remove print statementsAlexander Kabui
2021-06-15Fix issue where column values were used as str instead of bytes; pretty sure ↵zsloan
this was introduced by Python3
2021-05-08utility: startup_config: Use python3 f-stringsBonfaceKilz
2021-05-08utility: startup_config: Break up long import statementBonfaceKilz
2021-05-08utility: startup_config: Remove dead commentsBonfaceKilz
2021-05-07Fixed issue that caused /submit_trait page to not load properlyzsloan
2021-04-30autopep8: Run autopep8 100 times with target rulesBonfaceKilz
Rules used are: E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,E242, E251,E252,E26,E265,E266,E27,E301,E302,E303,E304,E305,E306, E401,E501,E70,E701,W291,W292,W293,W391,W504,E101,E11,E121, E122,E123,E124,E125,E126,E127,E128,E129,E131,E133
2021-04-30autopep8: Fix E121,E122,E123,EI24,E125,E126,E127,E128,E129,E131,E133BonfaceKilz
2021-04-30autopep8: Fix E101, E11BonfaceKilz
2021-04-30autopep8: Fix W504BonfaceKilz
2021-04-30autopep8: Fix W291, W292, W293, W391BonfaceKilz
2021-04-30autopep8: Fix E70 and E701BonfaceKilz
2021-04-30autopep8: Fix E501BonfaceKilz
2021-04-30autopep8: Fix E301,E302,E303,E304,E305,E306BonfaceKilz
2021-04-30autopep8: Fix E20-E27BonfaceKilz
Run: python -m autopep8 --in-place --recrusive ./ --select\ E20,E211,E22,E224,E224,E225,E226,E227,E228,E231,E241,\ E242,E251,E252,E26,E265,E266,E27 -p 3
2021-04-29Merge branch 'testing' into Feature/Add-upload-data-formsBonfaceKilz
2021-04-29Run `sed -i 's/(object)//g'`BonfaceKilz
See: https://is.gd/pL7IJF Ran: find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
2021-04-23Apply PEP-8BonfaceKilz
2021-04-23Move looped sql query into one statement in "get_species_groups"BonfaceKilz
It's in-efficient to have a sql query executed in a loop. As data grows, the query becomes slower. It's better to let sql handle such queries.
2021-04-23Remove stale commentsBonfaceKilz
2021-04-19Specify only getting the first two items after splitting the trait/dataset ↵zsloan
input string
2021-03-16Fixed encoding in load_json_from_redis to account for the first that column ↵zsloan
values are sometimes stored as bytes and sometimes as strings
2021-03-16Fixed encoding to make get_user_groups work properly, since the user IDs for ↵zsloan
groups in Redis are stored as strings
2021-03-16Removed unnecessary encoding of user_id from authentication_tools.pyzsloan
2021-02-18Remove the deocde since it was throwing an errorzsloan
2021-02-18Changed authentication_tools.py to account for encoding str as bytes and ↵zsloan
dealing with the permissions response either being a list or not a list (this should be temporary until I figure out what is going on here)
2021-02-17Fixed error caused by user IDs being encoded as byteszsloan
2021-01-06replace vars with vars_obj which is a function name in pythonAlexanderkabui
2020-12-18Added redirect_uri to the ORCID_AUTH_URL since it wasn't working due to ↵zsloan
missing this parameter
2020-11-02Created function for encoding the column value as bytes when fetching from ↵zsloan
the JSON-formatted string pulled from Redis (since this was needed after the Python 3 switchover) * wqflask/utility/redis_tools.py - Created function load_json_from_redis that encodes the key (column_value) when fetching a value from the JSON pulled from Redis
2020-10-28Use latin-1 encoding when converting hmac secret to bytesBonfaceKilz
* wqflask/utility/hmac.py (hmac_creation): Use latin-1 when serializing the hmac secret. This ensures that the behaviour of *verify_cookie* remains the same as in the python2 tip.
2020-09-26Merge branch 'testing' into build/python3-migrationBonfaceKilz
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Replace string arguments to "hmac.new" with bytearrayBonfaceKilz
Same as: https://github.com/genenetwork/genenetwork2/pull/422/commits/46443ec8d2cdfd7c60358a889d90a90e4f7daaf4
2020-09-17Apply pep8BonfaceKilz
* wqflask/base/trait.py: Apply pep8. * wqflask/utility/authentication_tools.py: Ditto.
2020-09-17Merge branch 'testing' into build/python3-migrationBonfaceKilz
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 23:29:36 +0000